**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=3d2g.pdb -o=3d2g.out File name: 3d2g.pdb no. of DNA/RNA chains: 2 [A=77,B=77] no. of nucleotides: 154 no. of atoms: 3535 no. of waters: 163 no. of metals: 10 [Mg=10] **************************************************************************** List of 73 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G3 A.C77 G-C WC 19-XIX cWW cW-W 2 A.A4 A.U76 A-U WC 20-XX cWW cW-W 3 A.C5 A.G75 C-G WC 19-XIX cWW cW-W 4 A.C6 A.G73 C-G WC 19-XIX cWW cW-W 5 A.A7 A.U39 A-U WC 20-XX cWW cW-W 6 A.G8 A.C38 G-C WC 19-XIX cWW cW-W 7 A.G8 A.A72 G-A -- -- cSS cm-m 8 A.G9 A.C37 G-C WC 19-XIX cWW cW-W 9 A.G9 A.A44 G+A Linker -- tSS tm+m 10 A.G10 A.C36 G-C WC 19-XIX cWW cW-W 11 A.G11 A.G30 G+G -- 04-IV tSS tm+m 12 A.G11 A.G34 G+G -- -- tW. tW+. 13 A.U12 A.A33 U+A Hoogsteen 23-XXIII cWH cW+M 14 A.G13 A.C26 G-C WC 19-XIX cWW cW-W 15 A.G13 A.U59 G-U -- -- cSS cm-m 16 A.C14 A.G25 C-G WC 19-XIX cWW cW-W 17 A.U15 A.G24 U-G Wobble 28-XXVIII cWW cW-W 18 A.U16 A.A23 U-A WC 20-XX cWW cW-W 19 A.G17 A.C22 G-C WC 19-XIX cWW cW-W 20 A.U19 A.A21 U+A Hoogsteen 23-XXIII cWH cW+M 21 A.G25 A.A57 G+A -- -- tSW tm+W 22 A.U27 A.A31 U-A rHoogsteen 24-XXIV tWH tW-M 23 A.A29 A.C36 A-C -- -- cSS cm-m 24 A.C38 A.A72 C+A -- -- tSW tm+W 25 A.G42 A.A72 G-A Sheared 11-XI tSH tm-M 26 A.A43 A.A68 A-A -- 05-V tWH tW-M 27 A.A44 A.G71 A-G Sheared 11-XI tHS tM-m 28 A.C45 A.G70 C-G WC 19-XIX cWW cW-W 29 A.C46 A.G69 C-G WC 19-XIX cWW cW-W 30 A.U47 A.A68 U-A WC 20-XX cWW cW-W 31 A.G48 A.G66 G+G Metal 06-VI cWH cW+M 32 A.A49 A.C65 A+C -- -- tW. tW+. 33 A.C51 A.G64 C-G WC 19-XIX cWW cW-W 34 A.A52 A.U63 A-U WC 20-XX cWW cW-W 35 A.G53 A.C62 G-C WC 19-XIX cWW cW-W 36 A.G54 A.C61 G-C WC 19-XIX cWW cW-W 37 A.U56 A.A58 U-A -- -- tSH tm-M 38 B.G3 B.C77 G-C WC 19-XIX cWW cW-W 39 B.A4 B.U76 A-U WC 20-XX cWW cW-W 40 B.C5 B.G75 C-G WC 19-XIX cWW cW-W 41 B.C6 B.G73 C-G WC 19-XIX cWW cW-W 42 B.A7 B.U39 A-U WC 20-XX cWW cW-W 43 B.G8 B.C38 G-C WC 19-XIX cWW cW-W 44 B.G8 B.A72 G-A -- -- cSS cm-m 45 B.G9 B.C37 G-C WC 19-XIX cWW cW-W 46 B.G9 B.A44 G+A Linker -- tSS tm+m 47 B.G10 B.C36 G-C WC 19-XIX cWW cW-W 48 B.G11 B.G30 G+G -- 04-IV tSS tm+m 49 B.G11 B.G34 G+G -- -- cW. cW+. 50 B.U12 B.A33 U+A Hoogsteen 23-XXIII cWH cW+M 51 B.G13 B.C26 G-C WC 19-XIX cWW cW-W 52 B.G13 B.U59 G-U -- -- cSS cm-m 53 B.C14 B.G25 C-G WC 19-XIX cWW cW-W 54 B.U15 B.G24 U-G Wobble 28-XXVIII cWW cW-W 55 B.U16 B.A23 U-A WC 20-XX cWW cW-W 56 B.G17 B.C22 G-C WC 19-XIX cWW cW-W 57 B.U19 B.A21 U+A Hoogsteen 23-XXIII cWH cW+M 58 B.G25 B.A57 G+A -- -- tSW tm+W 59 B.U27 B.A31 U-A rHoogsteen 24-XXIV tWH tW-M 60 B.A29 B.C36 A-C -- -- cSS cm-m 61 B.C38 B.A72 C+A -- -- tSW tm+W 62 B.G42 B.A72 G-A Sheared 11-XI tSH tm-M 63 B.A43 B.A68 A-A -- 05-V tWH tW-M 64 B.A44 B.G71 A-G Sheared 11-XI tHS tM-m 65 B.C45 B.G70 C-G WC 19-XIX cWW cW-W 66 B.C46 B.G69 C-G WC 19-XIX cWW cW-W 67 B.U47 B.A68 U-A WC 20-XX cWW cW-W 68 B.G48 B.G66 G+G Metal 06-VI cWH cW+M 69 B.A49 B.C65 A+C -- -- tW. tW+. 70 B.C51 B.G64 C-G WC 19-XIX cWW cW-W 71 B.A52 B.U63 A-U WC 20-XX cWW cW-W 72 B.G53 B.C62 G-C WC 19-XIX cWW cW-W 73 B.G54 B.C61 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 14 multiplets 1 nts=3 GAC A.G10,A.A29,A.C36 2 nts=3 GGG A.G11,A.G30,A.G34 3 nts=3 GCU A.G13,A.C26,A.U59 4 nts=3 CGA A.C14,A.G25,A.A57 5 nts=3 AUA A.A43,A.U47,A.A68 6 nts=3 GAC B.G10,B.A29,B.C36 7 nts=3 GGG B.G11,B.G30,B.G34 8 nts=3 GCU B.G13,B.C26,B.U59 9 nts=3 CGA B.C14,B.G25,B.A57 10 nts=3 AUA B.A43,B.U47,B.A68 11 nts=4 GCGA A.G8,A.C38,A.G42,A.A72 12 nts=4 GCAG A.G9,A.C37,A.A44,A.G71 13 nts=4 GCGA B.G8,B.C38,B.G42,B.A72 14 nts=4 GCAG B.G9,B.C37,B.A44,B.G71 **************************************************************************** List of 6 helices Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[2] bps=10 strand-1 5'-GACCAGGGGU-3' bp-type ||||||||.. strand-2 3'-CUGGUCCCGA-5' helix-form AAxxAAAx. 1 A.G3 A.C77 G-C WC 19-XIX cWW cW-W 2 A.A4 A.U76 A-U WC 20-XX cWW cW-W 3 A.C5 A.G75 C-G WC 19-XIX cWW cW-W 4 A.C6 A.G73 C-G WC 19-XIX cWW cW-W 5 A.A7 A.U39 A-U WC 20-XX cWW cW-W 6 A.G8 A.C38 G-C WC 19-XIX cWW cW-W 7 A.G9 A.C37 G-C WC 19-XIX cWW cW-W 8 A.G10 A.C36 G-C WC 19-XIX cWW cW-W 9 A.G11 A.G34 G+G -- -- tW. tW+. 10 A.U12 A.A33 U+A Hoogsteen 23-XXIII cWH cW+M -------------------------------------------------------------------------- helix#2[1] bps=7 strand-1 5'-ACAGGCU-3' bp-type .|||||. strand-2 3'-UGUUCGA-5' helix-form xA..Ax 1 A.A21 A.U19 A+U Hoogsteen 23-XXIII cHW cM+W 2 A.C22 A.G17 C-G WC 19-XIX cWW cW-W 3 A.A23 A.U16 A-U WC 20-XX cWW cW-W 4 A.G24 A.U15 G-U Wobble 28-XXVIII cWW cW-W 5 A.G25 A.C14 G-C WC 19-XIX cWW cW-W 6 A.C26 A.G13 C-G WC 19-XIX cWW cW-W 7 A.U27 A.A31 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#3[2] bps=11 strand-1 5'-GACCUGACAGG-3' bp-type ..|||..|||| strand-2 3'-AGGGAGCGUCC-5' helix-form x...x.xA.A 1 A.G42 A.A72 G-A Sheared 11-XI tSH tm-M 2 A.A44 A.G71 A-G Sheared 11-XI tHS tM-m 3 A.C45 A.G70 C-G WC 19-XIX cWW cW-W 4 A.C46 A.G69 C-G WC 19-XIX cWW cW-W 5 A.U47 A.A68 U-A WC 20-XX cWW cW-W 6 A.G48 A.G66 G+G Metal 06-VI cWH cW+M 7 A.A49 A.C65 A+C -- -- tW. tW+. 8 A.C51 A.G64 C-G WC 19-XIX cWW cW-W 9 A.A52 A.U63 A-U WC 20-XX cWW cW-W 10 A.G53 A.C62 G-C WC 19-XIX cWW cW-W 11 A.G54 A.C61 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[2] bps=10 strand-1 5'-GACCAGGGGU-3' bp-type ||||||||.. strand-2 3'-CUGGUCCCGA-5' helix-form A.xxAAAx. 1 B.G3 B.C77 G-C WC 19-XIX cWW cW-W 2 B.A4 B.U76 A-U WC 20-XX cWW cW-W 3 B.C5 B.G75 C-G WC 19-XIX cWW cW-W 4 B.C6 B.G73 C-G WC 19-XIX cWW cW-W 5 B.A7 B.U39 A-U WC 20-XX cWW cW-W 6 B.G8 B.C38 G-C WC 19-XIX cWW cW-W 7 B.G9 B.C37 G-C WC 19-XIX cWW cW-W 8 B.G10 B.C36 G-C WC 19-XIX cWW cW-W 9 B.G11 B.G34 G+G -- -- cW. cW+. 10 B.U12 B.A33 U+A Hoogsteen 23-XXIII cWH cW+M -------------------------------------------------------------------------- helix#5[1] bps=7 strand-1 5'-ACAGGCU-3' bp-type .|||||. strand-2 3'-UGUUCGA-5' helix-form xA..Ax 1 B.A21 B.U19 A+U Hoogsteen 23-XXIII cHW cM+W 2 B.C22 B.G17 C-G WC 19-XIX cWW cW-W 3 B.A23 B.U16 A-U WC 20-XX cWW cW-W 4 B.G24 B.U15 G-U Wobble 28-XXVIII cWW cW-W 5 B.G25 B.C14 G-C WC 19-XIX cWW cW-W 6 B.C26 B.G13 C-G WC 19-XIX cWW cW-W 7 B.U27 B.A31 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#6[2] bps=11 strand-1 5'-GACCUGACAGG-3' bp-type ..|||..|||| strand-2 3'-AGGGAGCGUCC-5' helix-form x...x.xAAA 1 B.G42 B.A72 G-A Sheared 11-XI tSH tm-M 2 B.A44 B.G71 A-G Sheared 11-XI tHS tM-m 3 B.C45 B.G70 C-G WC 19-XIX cWW cW-W 4 B.C46 B.G69 C-G WC 19-XIX cWW cW-W 5 B.U47 B.A68 U-A WC 20-XX cWW cW-W 6 B.G48 B.G66 G+G Metal 06-VI cWH cW+M 7 B.A49 B.C65 A+C -- -- tW. tW+. 8 B.C51 B.G64 C-G WC 19-XIX cWW cW-W 9 B.A52 B.U63 A-U WC 20-XX cWW cW-W 10 B.G53 B.C62 G-C WC 19-XIX cWW cW-W 11 B.G54 B.C61 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 10 stems Note: a stem is defined as a helix consisting of only canonical WC/wobble pairs, with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=3 strand-1 5'-GAC-3' bp-type ||| strand-2 3'-CUG-5' helix-form AA 1 A.G3 A.C77 G-C WC 19-XIX cWW cW-W 2 A.A4 A.U76 A-U WC 20-XX cWW cW-W 3 A.C5 A.G75 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-AGGG-3' bp-type |||| strand-2 3'-UCCC-5' helix-form AAA 1 A.A7 A.U39 A-U WC 20-XX cWW cW-W 2 A.G8 A.C38 G-C WC 19-XIX cWW cW-W 3 A.G9 A.C37 G-C WC 19-XIX cWW cW-W 4 A.G10 A.C36 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=5 strand-1 5'-GCUUG-3' bp-type ||||| strand-2 3'-CGGAC-5' helix-form A..A 1 A.G13 A.C26 G-C WC 19-XIX cWW cW-W 2 A.C14 A.G25 C-G WC 19-XIX cWW cW-W 3 A.U15 A.G24 U-G Wobble 28-XXVIII cWW cW-W 4 A.U16 A.A23 U-A WC 20-XX cWW cW-W 5 A.G17 A.C22 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#3] bps=3 strand-1 5'-CCU-3' bp-type ||| strand-2 3'-GGA-5' helix-form .. 1 A.C45 A.G70 C-G WC 19-XIX cWW cW-W 2 A.C46 A.G69 C-G WC 19-XIX cWW cW-W 3 A.U47 A.A68 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#3] bps=4 strand-1 5'-CAGG-3' bp-type |||| strand-2 3'-GUCC-5' helix-form A.A 1 A.C51 A.G64 C-G WC 19-XIX cWW cW-W 2 A.A52 A.U63 A-U WC 20-XX cWW cW-W 3 A.G53 A.C62 G-C WC 19-XIX cWW cW-W 4 A.G54 A.C61 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#4] bps=3 strand-1 5'-GAC-3' bp-type ||| strand-2 3'-CUG-5' helix-form A. 1 B.G3 B.C77 G-C WC 19-XIX cWW cW-W 2 B.A4 B.U76 A-U WC 20-XX cWW cW-W 3 B.C5 B.G75 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#4] bps=4 strand-1 5'-AGGG-3' bp-type |||| strand-2 3'-UCCC-5' helix-form AAA 1 B.A7 B.U39 A-U WC 20-XX cWW cW-W 2 B.G8 B.C38 G-C WC 19-XIX cWW cW-W 3 B.G9 B.C37 G-C WC 19-XIX cWW cW-W 4 B.G10 B.C36 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#5] bps=5 strand-1 5'-GCUUG-3' bp-type ||||| strand-2 3'-CGGAC-5' helix-form A..A 1 B.G13 B.C26 G-C WC 19-XIX cWW cW-W 2 B.C14 B.G25 C-G WC 19-XIX cWW cW-W 3 B.U15 B.G24 U-G Wobble 28-XXVIII cWW cW-W 4 B.U16 B.A23 U-A WC 20-XX cWW cW-W 5 B.G17 B.C22 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#6] bps=3 strand-1 5'-CCU-3' bp-type ||| strand-2 3'-GGA-5' helix-form .. 1 B.C45 B.G70 C-G WC 19-XIX cWW cW-W 2 B.C46 B.G69 C-G WC 19-XIX cWW cW-W 3 B.U47 B.A68 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#10[#6] bps=4 strand-1 5'-CAGG-3' bp-type |||| strand-2 3'-GUCC-5' helix-form AAA 1 B.C51 B.G64 C-G WC 19-XIX cWW cW-W 2 B.A52 B.U63 A-U WC 20-XX cWW cW-W 3 B.G53 B.C62 G-C WC 19-XIX cWW cW-W 4 B.G54 B.C61 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 isolated WC/wobble pairs Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 A.C6 A.G73 C-G WC 19-XIX cWW cW-W [#4] -2 B.C6 B.G73 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 4 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#2] 2 Helix#3 contains 2 stems: [#4,#5] 3 Helix#4 contains 2 stems: [#6,#7] 4 Helix#6 contains 2 stems: [#9,#10] **************************************************************************** List of 33 base stacks Note: a stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 CC A.C5,A.C6 2 nts=2 GA A.G13,A.A31 3 nts=2 GU A.G17,A.U19 4 nts=2 AC A.A21,A.C22 5 nts=2 AG A.A29,A.G30 6 nts=2 AA A.A50,B.A50 7 nts=2 GA B.G13,B.A31 8 nts=2 AC B.A21,B.C22 9 nts=2 AG B.A29,B.G30 10 nts=2 GG B.G73,B.G75 11 nts=3 GGG A.G1,A.G2,A.G3 12 nts=3 AGG A.A7,A.G73,A.G75 13 nts=3 CUG A.C26,A.U27,A.G28 14 nts=3 AGC A.A33,A.G34,A.C36 15 nts=3 CAA A.C45,A.A44,A.A72 16 nts=3 GGU A.G54,A.G55,A.U56 17 nts=3 AAU A.A57,A.A58,A.U59 18 nts=3 GGG B.G1,B.G2,B.G3 19 nts=3 CCA B.C5,B.C6,B.A7 20 nts=3 GUC B.G17,B.U19,B.C20 21 nts=3 CUG B.C26,B.U27,B.G28 22 nts=3 AGC B.A33,B.G34,B.C36 23 nts=3 CAA B.C45,B.A44,B.A72 24 nts=3 GGU B.G54,B.G55,B.U56 25 nts=3 AAU B.A57,B.A58,B.U59 26 nts=4 GGUA A.G10,A.G11,A.U12,A.A32 27 nts=4 UGGG A.U40,A.G42,A.G71,A.G70 28 nts=4 AGCG A.A43,A.G66,A.C65,A.G64 29 nts=4 UGAC A.U47,A.G48,A.A49,A.C51 30 nts=4 GGUA B.G10,B.G11,B.U12,B.A32 31 nts=4 UGGG B.U40,B.G42,B.G71,B.G70 32 nts=4 AGCG B.A43,B.G66,B.C65,B.G64 33 nts=4 UGAC B.U47,B.G48,B.A49,B.C51 **************************************************************************** Nucleotides not involved in stacking interactions nts=15 UCUUGCCUUUUGCCU A.U18,A.C20,A.U35,A.U41,A.G60,A.C61,A.C67,A.U74,B.U18,B.U35,B.U41,B.G60,B.C61,B.C67,B.U74 **************************************************************************** List of 15 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.C22 A.A21 3.42 2 phosphate OP2@A.G30 A.G28 3.23 3 other N3'@A.TPP83 A.G30 3.33 4 other N3'@A.TPP83 A.A31 3.37 5 sugar O4'@A.C36 A.G34 3.16 6 sugar O4'@A.U40 A.G42 3.05 7 sugar O2'@A.C38 A.A44 3.46 8 phosphate OP2@A.A58 A.U56 2.98 9 sugar O4'@A.U39 A.A72 3.17 10 phosphate OP2@B.G30 B.G28 3.05 11 other N3'@B.TPP83 B.G30 3.29 12 other N3'@B.TPP83 B.A31 3.44 13 sugar O4'@B.C36 B.G34 3.41 14 sugar O4'@B.U40 B.G42 3.09 15 phosphate OP2@B.A58 B.U56 2.74 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 4 hairpin loops 1 hairpin loop: nts=6; [4]; linked by [#3] summary: [1] 4 [A.17 A.22] 5 nts=6 GUUCAC A.G17,A.U18,A.U19,A.C20,A.A21,A.C22 nts=4 UUCA A.U18,A.U19,A.C20,A.A21 2 hairpin loop: nts=8; [6]; linked by [#5] summary: [1] 6 [A.54 A.61] 4 nts=8 GGUAAUGC A.G54,A.G55,A.U56,A.A57,A.A58,A.U59,A.G60,A.C61 nts=6 GUAAUG A.G55,A.U56,A.A57,A.A58,A.U59,A.G60 3 hairpin loop: nts=6; [4]; linked by [#8] summary: [1] 4 [B.17 B.22] 5 nts=6 GUUCAC B.G17,B.U18,B.U19,B.C20,B.A21,B.C22 nts=4 UUCA B.U18,B.U19,B.C20,B.A21 4 hairpin loop: nts=8; [6]; linked by [#10] summary: [1] 6 [B.54 B.61] 4 nts=8 GGUAAUGC B.G54,B.G55,B.U56,B.A57,B.A58,B.U59,B.G60,B.C61 nts=6 GUAAUG B.G55,B.U56,B.A57,B.A58,B.U59,B.G60 **************************************************************************** List of 2 bulges 1 bulge: nts=5; [0,1]; linked by [#1,#-1] summary: [2] 0 1 [A.5 A.75 A.6 A.73] 3 1 nts=5 CCGUG A.C5,A.C6,A.G73,A.U74,A.G75 nts=0 nts=1 U A.U74 2 bulge: nts=5; [0,1]; linked by [#6,#-2] summary: [2] 0 1 [B.5 B.75 B.6 B.73] 3 1 nts=5 CCGUG B.C5,B.C6,B.G73,B.U74,B.G75 nts=0 nts=1 U B.U74 **************************************************************************** List of 4 internal loops 1 symmetric internal loop: nts=10; [3,3]; linked by [#4,#5] summary: [2] 3 3 [A.47 A.68 A.51 A.64] 3 4 nts=10 UGAACGCGCA A.U47,A.G48,A.A49,A.A50,A.C51,A.G64,A.C65,A.G66,A.C67,A.A68 nts=3 GAA A.G48,A.A49,A.A50 nts=3 CGC A.C65,A.G66,A.C67 2 symmetric internal loop: nts=10; [3,3]; linked by [#9,#10] summary: [2] 3 3 [B.47 B.68 B.51 B.64] 3 4 nts=10 UGAACGCGCA B.U47,B.G48,B.A49,B.A50,B.C51,B.G64,B.C65,B.G66,B.C67,B.A68 nts=3 GAA B.G48,B.A49,B.A50 nts=3 CGC B.C65,B.G66,B.C67 3 asymmetric internal loop: nts=15; [2,9]; linked by [#2,#3] summary: [2] 2 9 [A.10 A.36 A.13 A.26] 4 5 nts=15 GGUGCUGAGAAAGUC A.G10,A.G11,A.U12,A.G13,A.C26,A.U27,A.G28,A.A29,A.G30,A.A31,A.A32,A.A33,A.G34,A.U35,A.C36 nts=2 GU A.G11,A.U12 nts=9 UGAGAAAGU A.U27,A.G28,A.A29,A.G30,A.A31,A.A32,A.A33,A.G34,A.U35 4 asymmetric internal loop: nts=15; [2,9]; linked by [#7,#8] summary: [2] 2 9 [B.10 B.36 B.13 B.26] 4 5 nts=15 GGUGCUGAGAAAGUC B.G10,B.G11,B.U12,B.G13,B.C26,B.U27,B.G28,B.A29,B.G30,B.A31,B.A32,B.A33,B.G34,B.U35,B.C36 nts=2 GU B.G11,B.U12 nts=9 UGAGAAAGU B.U27,B.G28,B.A29,B.G30,B.A31,B.A32,B.A33,B.G34,B.U35 **************************************************************************** List of 2 junctions 1 3-way junction: nts=13; [0,5,2]; linked by [#-1,#2,#4] summary: [3] 0 5 2 [A.6 A.73 A.7 A.39 A.45 A.70] 1 4 3 nts=13 CAUUUGAACGGAG A.C6,A.A7,A.U39,A.U40,A.U41,A.G42,A.A43,A.A44,A.C45,A.G70,A.G71,A.A72,A.G73 nts=0 nts=5 UUGAA A.U40,A.U41,A.G42,A.A43,A.A44 nts=2 GA A.G71,A.A72 2 3-way junction: nts=13; [0,5,2]; linked by [#-2,#7,#9] summary: [3] 0 5 2 [B.6 B.73 B.7 B.39 B.45 B.70] 1 4 3 nts=13 CAUUUGAACGGAG B.C6,B.A7,B.U39,B.U40,B.U41,B.G42,B.A43,B.A44,B.C45,B.G70,B.G71,B.A72,B.G73 nts=0 nts=5 UUGAA B.U40,B.U41,B.G42,B.A43,B.A44 nts=2 GA B.G71,B.A72 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 GG A.G1,A.G2 2 nts=2 GG B.G1,B.G2 **************************************************************************** List of 12 A-minor motifs (types I, II, or X) 1 type=II A|G-C A.A29|A.G10,A.C36 WC +A.G10 H-bonds[0]: "" -A.C36 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.89],N3-O2'(hydroxyl)[2.72]" 2 type=X A|G-C A.A31|A.G13,A.C26 WC +A.G13 H-bonds[2]: "O2'(hydroxyl)-N7[3.27],O2'(hydroxyl)-O6(carbonyl)[2.72]" -A.C26 H-bonds[0]: "" 3 type=I A|G-C A.A44|A.G9,A.C37 WC +A.G9 H-bonds[2]: "N1-O2'(hydroxyl)[2.92],N3-N2(amino)[2.73]" -A.C37 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.81],O2'(hydroxyl)-O2(carbonyl)[3.04]" 4 type=X A|C-G A.A57|A.C14,A.G25 WC -A.C14 H-bonds[0]: "" +A.G25 H-bonds[1]: "N1-N2(amino)[3.36]" 5 type=II A|C-G A.A58|A.C14,A.G25 WC -A.C14 H-bonds[3]: "O2'(hydroxyl)-O3'[3.06],O2'(hydroxyl)-O2'(hydroxyl)[2.86],N3-O2'(hydroxyl)[3.10]" +A.G25 H-bonds[0]: "" 6 type=I A|G-C A.A72|A.G8,A.C38 WC -A.G8 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.54],N3-N2(amino)[3.07]" +A.C38 H-bonds[1]: "N1-O2'(hydroxyl)[2.71]" 7 type=II A|G-C B.A29|B.G10,B.C36 WC +B.G10 H-bonds[0]: "" -B.C36 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.75],N3-O2'(hydroxyl)[2.77]" 8 type=X A|G-C B.A31|B.G13,B.C26 WC +B.G13 H-bonds[2]: "O2'(hydroxyl)-N7[2.90],O2'(hydroxyl)-O6(carbonyl)[3.20]" -B.C26 H-bonds[0]: "" 9 type=I A|G-C B.A44|B.G9,B.C37 WC +B.G9 H-bonds[2]: "N1-O2'(hydroxyl)[3.06],N3-N2(amino)[3.10]" -B.C37 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.14],O2'(hydroxyl)-O2(carbonyl)[3.08]" 10 type=X A|C-G B.A57|B.C14,B.G25 WC -B.C14 H-bonds[0]: "" +B.G25 H-bonds[1]: "N1-N2(amino)[3.15]" 11 type=II A|C-G B.A58|B.C14,B.G25 WC -B.C14 H-bonds[3]: "O2'(hydroxyl)-O3'[2.98],O2'(hydroxyl)-O2'(hydroxyl)[2.75],N3-O2'(hydroxyl)[2.87]" +B.G25 H-bonds[0]: "" 12 type=I A|G-C B.A72|B.G8,B.C38 WC -B.G8 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.39],N3-N2(amino)[3.22]" +B.C38 H-bonds[1]: "N1-O2'(hydroxyl)[2.88]" **************************************************************************** List of 2 ribose zippers 1 nts=4 GCAU A.G13,A.C14,A.A58,A.U59 2 nts=4 GCAU B.G13,B.C14,B.A58,B.U59 **************************************************************************** List of 26 splayed-apart dinucleotides 1 A.U12 A.G13 angle=90 distance=13.7 ratio=0.71 2 A.U39 A.U40 angle=96 distance=13.7 ratio=0.74 3 A.U40 A.U41 angle=145 distance=18.8 ratio=0.95 4 A.U41 A.G42 angle=129 distance=17.2 ratio=0.90 5 A.G42 A.A43 angle=89 distance=12.1 ratio=0.70 6 A.A49 A.A50 angle=132 distance=17.8 ratio=0.92 7 A.A50 A.C51 angle=164 distance=18.5 ratio=0.99 8 A.U59 A.G60 angle=89 distance=12.8 ratio=0.70 9 A.G60 A.C61 angle=124 distance=15.4 ratio=0.88 10 A.G66 A.C67 angle=157 distance=19.5 ratio=0.98 11 A.C67 A.A68 angle=139 distance=19.9 ratio=0.94 12 A.G73 A.U74 angle=102 distance=16.3 ratio=0.78 13 A.U74 A.G75 angle=125 distance=15.8 ratio=0.89 14 B.U12 B.G13 angle=90 distance=13.6 ratio=0.71 15 B.U39 B.U40 angle=90 distance=13.1 ratio=0.71 16 B.U40 B.U41 angle=149 distance=18.4 ratio=0.96 17 B.U41 B.G42 angle=126 distance=17.0 ratio=0.89 18 B.G42 B.A43 angle=89 distance=12.0 ratio=0.70 19 B.A49 B.A50 angle=131 distance=17.5 ratio=0.91 20 B.A50 B.C51 angle=166 distance=18.4 ratio=0.99 21 B.U59 B.G60 angle=91 distance=11.9 ratio=0.72 22 B.G60 B.C61 angle=111 distance=13.9 ratio=0.83 23 B.G66 B.C67 angle=165 distance=20.2 ratio=0.99 24 B.C67 B.A68 angle=145 distance=20.3 ratio=0.95 25 B.G73 B.U74 angle=101 distance=15.4 ratio=0.78 26 B.U74 B.G75 angle=110 distance=15.4 ratio=0.82 ---------------------------------------------------------------- Summary of 12 splayed-apart units 1 nts=2 UG A.U12,A.G13 2 nts=5 UUUGA A.U39,A.U40,A.U41,A.G42,A.A43 3 nts=3 AAC A.A49,A.A50,A.C51 4 nts=3 UGC A.U59,A.G60,A.C61 5 nts=3 GCA A.G66,A.C67,A.A68 6 nts=3 GUG A.G73,A.U74,A.G75 7 nts=2 UG B.U12,B.G13 8 nts=5 UUUGA B.U39,B.U40,B.U41,B.G42,B.A43 9 nts=3 AAC B.A49,B.A50,B.C51 10 nts=3 UGC B.U59,B.G60,B.C61 11 nts=3 GCA B.G66,B.C67,B.A68 12 nts=3 GUG B.G73,B.U74,B.G75 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3d2g nts=154 [whole] GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC&GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC ..((((((((..(((((....))))).........)))).....(((...((((......))))...)))..).)))&..((((((((..(((((....))))).........)))).....(((...((((......))))...)))..).))) >3d2g-A #1 nts=77 0.00(3.16) [chain] RNA GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC ..((((((((..(((((....))))).........)))).....(((...((((......))))...)))..).))) >3d2g-B #2 nts=77 0.02(3.07) [chain] RNA GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC ..((((((((..(((((....))))).........)))).....(((...((((......))))...)))..).))) **************************************************************************** Summary of structural features of 154 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G . A.G1 0.038 anti,~C3'-endo,non-pair-contact,ss-non-loop 2 G . A.G2 0.024 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 3 G ( A.G3 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 4 A ( A.A4 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( A.C5 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 6 C ( A.C6 0.018 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,junction-loop 7 A ( A.A7 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 8 G ( A.G8 0.032 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 9 G ( A.G9 0.021 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 10 G ( A.G10 0.035 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 11 G . A.G11 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 12 U . A.U12 0.032 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate,splayed-apart 13 G ( A.G13 0.024 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,ribose-zipper,splayed-apart 14 C ( A.C14 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 15 U ( A.U15 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 U ( A.U16 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 G ( A.G17 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 18 U . A.U18 0.023 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate 19 U . A.U19 0.021 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 20 C . A.C20 0.019 anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop 21 A . A.A21 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 22 C ) A.C22 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 23 A ) A.A23 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 24 G ) A.G24 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 25 G ) A.G25 0.026 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 26 C ) A.C26 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor 27 U . A.U27 0.025 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 28 G . A.G28 0.015 u-turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-acceptor 29 A . A.A29 0.030 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor 30 G . A.G30 0.036 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,cap-donor,cap-acceptor,phosphate 31 A . A.A31 0.023 turn,u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,cap-acceptor,phosphate 32 A . A.A32 0.023 turn,syn,~C2'-endo,non-pair-contact,internal-loop 33 A . A.A33 0.019 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 34 G . A.G34 0.013 syn,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,cap-acceptor 35 U . A.U35 0.018 turn,syn,~C2'-endo,BII,non-stack,internal-loop 36 C ) A.C36 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,cap-donor,phosphate 37 C ) A.C37 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 38 C ) A.C38 0.019 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,cap-donor 39 U ) A.U39 0.022 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 40 U . A.U40 0.021 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 41 U . A.U41 0.012 turn,anti,~C2'-endo,non-stack,junction-loop,splayed-apart 42 G . A.G42 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,phosphate,splayed-apart 43 A . A.A43 0.036 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 44 A . A.A44 0.032 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,cap-acceptor 45 C ( A.C45 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 46 C ( A.C46 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 U ( A.U47 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 48 G . A.G48 0.030 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 49 A . A.A49 0.051 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 50 A . A.A50 0.034 turn,anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 51 C ( A.C51 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 52 A ( A.A52 0.049 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 53 G ( A.G53 0.038 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 G ( A.G54 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 55 G . A.G55 0.027 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 56 U . A.U56 0.034 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,cap-acceptor 57 A . A.A57 0.029 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor 58 A . A.A58 0.026 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 59 U . A.U59 0.033 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,ribose-zipper,phosphate,splayed-apart 60 G . A.G60 0.036 turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 61 C ) A.C61 0.035 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,phosphate,splayed-apart 62 C ) A.C62 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 U ) A.U63 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 G ) A.G64 0.036 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 65 C . A.C65 0.021 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 66 G . A.G66 0.037 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 67 C . A.C67 0.027 turn,anti,~C3'-endo,non-stack,internal-loop,splayed-apart 68 A ) A.A68 0.019 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,splayed-apart 69 G ) A.G69 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 G ) A.G70 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 71 G . A.G71 0.040 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 72 A . A.A72 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,cap-acceptor 73 G ) A.G73 0.024 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,splayed-apart 74 U . A.U74 0.014 turn,anti,non-stack,non-pair-contact,bulge,splayed-apart 75 G ) A.G75 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 76 U ) A.U76 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 77 C ) A.C77 0.008 anti,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 78 G . B.G1 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 79 G . B.G2 0.022 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 80 G ( B.G3 0.018 anti,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 81 A ( B.A4 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 82 C ( B.C5 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 83 C ( B.C6 0.006 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate 84 A ( B.A7 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 85 G ( B.G8 0.022 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 86 G ( B.G9 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 87 G ( B.G10 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 88 G . B.G11 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 89 U . B.U12 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,splayed-apart 90 G ( B.G13 0.024 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,ribose-zipper,splayed-apart 91 C ( B.C14 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 92 U ( B.U15 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 93 U ( B.U16 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 94 G ( B.G17 0.022 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 95 U . B.U18 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate 96 U . B.U19 0.016 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 97 C . B.C20 0.016 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 98 A . B.A21 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 99 C ) B.C22 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 100 A ) B.A23 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 101 G ) B.G24 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 102 G ) B.G25 0.024 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 103 C ) B.C26 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor 104 U . B.U27 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 105 G . B.G28 0.024 u-turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-acceptor 106 A . B.A29 0.025 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor 107 G . B.G30 0.018 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,cap-donor,cap-acceptor,phosphate 108 A . B.A31 0.020 turn,u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,cap-acceptor,phosphate 109 A . B.A32 0.013 turn,syn,~C2'-endo,non-pair-contact,internal-loop 110 A . B.A33 0.010 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 111 G . B.G34 0.021 ~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,cap-acceptor 112 U . B.U35 0.012 turn,syn,~C2'-endo,BII,non-stack,internal-loop 113 C ) B.C36 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,cap-donor,phosphate 114 C ) B.C37 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 115 C ) B.C38 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 116 U ) B.U39 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 117 U . B.U40 0.016 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 118 U . B.U41 0.013 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 119 G . B.G42 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,splayed-apart 120 A . B.A43 0.033 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 121 A . B.A44 0.035 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor 122 C ( B.C45 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 123 C ( B.C46 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 124 U ( B.U47 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 125 G . B.G48 0.031 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 126 A . B.A49 0.023 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 127 A . B.A50 0.033 turn,anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 128 C ( B.C51 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 129 A ( B.A52 0.036 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 130 G ( B.G53 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 131 G ( B.G54 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 132 G . B.G55 0.018 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 133 U . B.U56 0.014 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor 134 A . B.A57 0.049 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor 135 A . B.A58 0.020 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 136 U . B.U59 0.023 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,ribose-zipper,phosphate,splayed-apart 137 G . B.G60 0.022 turn,syn,~C3'-endo,BII,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 138 C ) B.C61 0.024 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,phosphate,splayed-apart 139 C ) B.C62 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 140 U ) B.U63 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 141 G ) B.G64 0.034 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 142 C . B.C65 0.035 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 143 G . B.G66 0.047 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 144 C . B.C67 0.028 turn,anti,~C2'-endo,non-stack,internal-loop,phosphate,splayed-apart 145 A ) B.A68 0.032 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,splayed-apart 146 G ) B.G69 0.032 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 147 G ) B.G70 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 148 G . B.G71 0.029 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 149 A . B.A72 0.029 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor 150 G ) B.G73 0.009 anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,splayed-apart 151 U . B.U74 0.007 turn,anti,non-stack,non-pair-contact,bulge,splayed-apart 152 G ) B.G75 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 153 U ) B.U76 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 154 C ) B.C77 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 16 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-bulges.pdb -- an ensemble of bulges 7 dssr-iloops.pdb -- an ensemble of internal loops 8 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 9 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 10 dssr-2ndstrs.ct -- secondary structure in connectivity table format 11 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 12 dssr-torsions.txt -- backbone torsion angles and suite names 13 dssr-splays.pdb -- an ensemble of splayed-apart units 14 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 15 dssr-stacks.pdb -- an ensemble of base stacks 16 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions